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Lecture 4: Phylogeny and the Tree of Life

Campbell & Reece:

Chapter 26

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HumansRattlesnakePine treeAmoebaBacterium

All life is interconnected by descent

How to determine the pattern of descent?

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Systematics - field of biology dealing with diversity and evolutionary history of life

Includes Taxonomy: DINCDescription Identification NomenclatureClassification

Goal:– Determine Evolutionary History (Phylogeny) of Life

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Description

= assign features

Character = a feature (e.g., “petal color”)

Character states = two or more forms of a character (e.g., “red,” “white”).

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Identification

= associate an unknown with a knownHow? One way: Taxonomic Key, e.g.,

Tree …………………………………….…………… Species A Leaves simple …….………………………… Species B Leaves pinnate …….………..…..…..…… Species C

Herb Flowers red …….…………………………… Species D Flowers white …….…………………..…… Species E

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Nomenclature

Naming, according to a formal system.

Binomial: Species are two names (Linnaeus):

E.g., Homo sapiensHomo = genus namesapiens = specific epithetHomo sapiens = species name

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Nomenclature

Hierarchical Ranks:Domain

KingdomPhylum

ClassOrder

FamilyGenus

Species

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Classification

• Placing objects, e.g., life, into some type of order.

• Taxon = a taxonomic group (plural = taxa).

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How to classify life

• Phenetic classification

– Based on overall similarity

– Those organisms most similar are classified more “closely” together.

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Problem with phenetic classification:• Can be arbitrary,

e.g., classify these:

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Phylogenetic classification

• Based on known (inferred) evolutionary history.

• Advantage:– Classification reflects pattern of evolution– Classification not ambiguous

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TIME

lineage or clade

Cladogram or Phylogenetic Tree

= representation of the history of life

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A B C D E F

TIME

lineage or clade

Cladogram or Phylogenetic Tree

TAXA

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A B C D E F

TIME

speciation

Cladogram or Phylogenetic Tree

TAXA

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Ingroup – group studied

Outgroup – group not part of ingroup, used to “root” tree

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Fig. 26-5

Sistertaxa

ANCESTRALLINEAGE

Taxon A

PolytomyCommon ancestor oftaxa A–F

Branch point(node)

Taxon B

Taxon C

Taxon D

Taxon E

Taxon F

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Apomorphy (derived trait)

= a new, derived feature= a new, derived featureE.g., for this evolutionary transformationE.g., for this evolutionary transformation

scales --------> feathers scales --------> feathers(ancestral feature)(ancestral feature) (derived feature) (derived feature)

Presence of feathers is an Presence of feathers is an apomorphyapomorphy for birds.for birds.

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Taxa are grouped by apomorphies

Apomorphies are the result of evolution.

Taxa sharing apomorphies underwent same evolutionary history should be grouped together.

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Principle of ParsimonyThat cladogram (tree) having the fewest number

of “steps” (evolutionary changes) is the one accepted.

Okham’s razor: the simplest explanation, with fewest number of “ad hoc” hypotheses, is accepted.

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Other methods of phylogeny reconstruction:

• Maximum Likelihood or Bayesian analysis– Uses probabilities– Advantage: can use evolutionary models.

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apomorphies (for Taxa B & C)

apomorphy(for Taxon D)

apomorphy (for Taxa B,C,D,E,F)

A B C D E F

TIME

Cladogram or Phylogenetic Tree

TAXA

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Fig. 26-11

TAXA

Lan

cele

t(o

utg

rou

p)

Lam

pre

y

Sal

aman

der

Leo

par

d

Tu

rtle

Tu

na

Vertebral column(backbone)

Hinged jaws

Four walking legs

Amniotic (shelled) egg

CH

AR

AC

TE

RS

Hair

(a) Character table

Hair

Hinged jaws

Vertebralcolumn

Four walking legs

Amniotic egg

(b) Phylogenetic tree

Salamander

Leopard

Turtle

Lamprey

Tuna

Lancelet(outgroup)

0

0 0

0

0

0

0 0

0

0

0 0

0 0 0 1

11

111

1

11

1

1

11

11

Sequentially group taxa by shared derived character states (apomorphies)

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Fig. 26-8a

Deletion

Insertion

1

2

DNA sequence data – most important type of data

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Fig. 26-8b

3

4

DNA sequence data - alignment

Each nucleotide position = CharacterCharacter states = specific nucleotide

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Homology

• Similarity resulting from common ancestry.

– E.g., the forelimb bones of a bird, bat, and cat.

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Homoplasy (analogy)

• Similarity not due to common ancestry

• Reversal – loss of new (apomorphic) feature, resembles ancestral (old) feature.

• Convergence (parallelism) – gain of new, similar features independently.

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Convergent evolution:spines of cacti & euphorbs

Cactus EuphorbEuphorb

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euphorb spines cactus spines

Convergent evolution:spines of cacti & euphorbs

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Both examples of reversal within Tetrapods: loss of a derived feature – forelimbs.

Leg-less lizards Snake

Example of convergence relative to one another!Independently evolved.

snakesleg-lesslizards

leggedlizards

**

*= loss of legs

gain of legs (Tetrapods)

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Convergent evolution:wings of some animals evolved independently

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Fig. 26-7

Convergent evolution:Australian “mole” and N. Am. “mole”

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Fig. 26-18

(b) Paralogous genes

(a) Orthologous genes

Ancestral gene

Paralogous genes

Ancestral species

Speciation withdivergence of gene

Gene duplication and divergence

Species A after many generations

Species A Species B

Species A

Orthologous genes

Orthology – genes homologous

Paralogy – genes not homologous

Gene Duplicationcan occur!

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A B C D E F

TIME

Cladogram or Phylogenetic Tree

TAXA

common ancestor (of taxon A & taxa B-F)

common ancestor (of taxon D, E, & F)

Common ancestry

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Monophyletic Group

• a group consisting of: – a common ancestor +– all descendents of that common ancestor

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monophyleticgroup

A B C D E F

TIME

Cladogram or Phylogenetic Tree

TAXA

common ancestor (of taxon A & taxa B-F)

common ancestor (of taxon D, E, & F)

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monophyleticgroup

A B C D E F

TIME

Cladogram or Phylogenetic Tree

TAXA

common ancestor (of taxon A & taxa B-F)

common ancestor (of taxon D, E, & F)

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monophyleticgroup

A B C D E F

TIME

Cladogram or Phylogenetic Tree

TAXA

common ancestor (of taxon A & taxa B-F)

common ancestor (of taxon D, E, & F)

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monophyleticgroup

A B C D E F

TIME

Cladogram or Phylogenetic Tree

TAXA

common ancestor (of taxon A & taxa B-F)

common ancestor (of taxon D, E, & F)

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monophyleticgroup

A B C D E F

TIME

Cladogram or Phylogenetic Tree

TAXA

common ancestor (of taxon A & taxa B-F)

common ancestor (of taxon D, E, & F)

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A B C D E F

TIME

speciation

Cladogram or Phylogenetic Tree

TAXA

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A B C D E F

TIME

speciation

Cladogram or Phylogenetic Tree

TAXA

C B F E D A

Cladograms can be “flipped” at nodes, show same relationships

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Fig. 26-13

Drosophila

Lancelet

Zebrafish

Frog

Human

Chicken

Mouse

CENOZOIC

Present65.5

MESOZOIC

251

Millions of years ago

PALEOZOIC

542

One can date divergence times with molecular clock and fossils

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Relationship

• = recency of common ancestry

i.e., taxa sharing a common ancestor more recent in time are more closely related than those sharing common ancestors more distant in time.

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Example:

• Are fish more closely related to sharks or to humans?

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Shark Fish Humans

TIME

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Shark Fish Humans

TIME

common ancestor of Fish and Humans

common ancestor of Sharks, Fish, and Humans

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monophyleticgroup

OsteichthyesVertebrata

Shark Fish Humans

TIME

common ancestor of Fish and Humans

common ancestor of Sharks, Fish, and Humans

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Example:

• Are crocodyles more closely related to lizards or to birds?

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Lizards & Snakes Crocodyles BirdsTurtles

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Lizards & Snakes Crocodyles BirdsTurtles

"Reptilia"

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Paraphyletic group

• Consist of common ancestor but not all descendents

• Paraphyletic groups are unnatural, distort evolutionary history, and should not be recognized.

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Lizards & Snakes Crocodyles BirdsTurtles

"Reptilia"

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Lizards & Snakes Crocodyles BirdsTurtles

"Reptilia"

“Reptilia” here paraphyletic

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Lizards & Snakes Crocodyles BirdsTurtles

Reptilia

Re-defined Reptilia monophyletic

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Lizards & Snakes Crocodyles BirdsTurtles

Dinosaurs

† † †

Reptilia

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Importance of a name:Did humans evolve from apes?

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Gorilla Chimpanzees HumansOrangatan

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Gorilla Chimpanzees HumansOrangatan

HominidaePongidae

“Great Apes”

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Hominidae

Gorilla Chimpanzees HumansOrangatan

Pongidae“Great Apes”Pongidae orHominidae

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Hominidae

Gorilla Chimpanzees HumansOrangatan

Pongidae orHominidae

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Hominidae

Gorilla Chimpanzees HumansOrangatan

Pongidae orHominidae

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We are human, butwe are also apes.

• We share unique human features.

• We also share features with other apes (and with other animals, plants, fungi, bacteria, etc.).

• Humans didn’t evolve from apes, humans are apes.

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Importance of systematics & evolution:

1) Foundation of biology - study of biodiversity2) Basis for classification of life3) Gives insight into biological processes:

speciation processesadaptation to environment

4) Can be aesthetically/intellectually pleasing!

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E.g., schistosomiasis

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Schistosomiasis:

knowledge of species diversity and evolutionary history of primary host can aid in controlling parasite

(Schistosoma, a fluke)

Phylogeny of Oncomelania snails

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All of life is interconnectedby descent.

A B C D E F

TIME

lineage or clade

Cladogram or Phylogenetic Tree

TAXA

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There are no “higher” or “lower” species.

A B C D E F

TIME

lineage or clade

Cladogram or Phylogenetic Tree

TAXA


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